Biology subjects

Shlezinger, N.

Publications and source records attributed to Shlezinger, N..

8 recordsLinked to original sources

bioRxiv2024

Exploring the trade-off between deep-learning and explainable models for brain-machine interfaces

People with brain or spinal cord-related paralysis often need to rely on others for basic tasks, limiting their independence. A potential solution is brain-machine interfaces (BMIs), which could allow them to voluntarily control external devices (e.g., robotic arm) by decoding brain activity to movement commands. In the past decade, deep-learning decoders have achieved state-of-the-art results in most BMI applications, ranging from speech production to finger control. However, the black-box nature of deep-learning decoders could lead to unexpected behaviors, resulting in major safety concerns in real-world physical control scenarios. In these applications, explainable but lower-performing decoders, such as the Kalman filter (KF), remain the norm. In this study, we designed a BMI decoder based on KalmanNet, an extension of the KF that augments its operation with recurrent neural networks to compute the Kalman gain. This results in a varying "trust" that shifts between inputs and dynamics. We used this algorithm to predict finger movements from the brain activity of two monkeys. We compared KalmanNet results offline (pre-recorded data, n = 13 days) and online (real-time predictions, n = 5 days) with a simple KF and two recent deep-learning algorithms with state-of-the-art results: tcFNN and LSTM. KalmanNet achieved comparable or better results than other deep learning models in offline and online modes, relying on the dynamical model for stopping while depending more on neural inputs for initiating movements. We further validated this mechanism by implementing a heteroscedastic KF that used the same strategy, and it also approached state-of-the-art performance while remaining in the explainable domain of standard KFs. However, we also see two downsides to KalmanNet. KalmanNet shares the limited generalization ability of existing deep-learning decoders, and its usage of the KF as an inductive bias limits its performance in the presence of unseen noise distributions. Despite this trade-off, our analysis successfully integrates traditional controls and modern deep-learning approaches to motivate high-performing yet still explainable BMI designs.

neuroscience↗

bioRxiv2024

Harnessing Random Peptide Mixtures to Overcome Multidrug-Resistant Fungal Infections

Invasive fungal infections are associated with high mortality and are increasingly difficult to treat due to a limited antifungal arsenal and the rapid emergence of drug resistance. Novel therapeutic strategies that combine potent antifungal activity, low host toxicity, in vivo stability, and a reduced propensity for resistance development are urgently needed. Antimicrobial peptides (AMPs) stand out as a promising class of compounds to combat antimicrobial resistance. Leveraging the unique properties of AMPs, we previously developed a novel approach to synthesize random peptide mixtures (RPMs) with robust bactericidal activity against drug-resistant bacteria. Here, we evaluate the antifungal potential of RPMs and demonstrate species-dependent, broad-spectrum activity of FK20 (L-phenylalanine-L-lysine, 20-mer) against major human fungal pathogens, including Candida spp., Cryptococcus neoformans, and Aspergillus fumigatus, with particularly high potency against the multidrug-resistant pathogen Candida auris. Mechanistic analyses revealed rapid membrane and cell wall disruption accompanied by intracellular penetration, consistent with membrane-active antifungal activity. Importantly, experimental evolution assays demonstrated a markedly reduced capacity for resistance development in C. auris. FK20 inhibited biofilm formation and displayed substantial activity against mature, pre-formed biofilms, both alone and synergistically in combination with caspofungin. Finally, FK20 showed significant therapeutic efficacy in a murine model of systemic candidiasis. Collectively, these findings establish RPMs as a versatile antifungal platform with broad-spectrum activity, biofilm efficacy, and a low resistance footprint, highlighting their promise as a novel therapeutic strategy against drug-resistant fungal infections. ImportanceThe rising prevalence of invasive fungal infections, particularly among immunocompromised individuals, has become a critical public health concern. However, antifungal drug development has not kept pace with this growing need, and treatment options remain limited to a small number of drug classes. The emergence of multidrug-resistant fungal pathogens, such as Candida auris, further exacerbates this crisis by reducing the efficacy of existing therapeutics and increasing the risk of treatment failure. In this study, we evaluate the antifungal potential of FK20, a random peptide mixture (RPM) composed of L-phenylalanine and L-lysine. FK20 displays potent activity against C. auris and other clinically relevant human fungal pathogens, impairs biofilm formation, and exhibits synergy with caspofungin. Importantly, FK20 limits the emergence of resistance and demonstrates therapeutic efficacy in a murine model of systemic candidiasis. These findings establish RPMs as a promising new class of antifungals with broad-spectrum activity and clinical potential against drug-resistant fungal infections.

microbiology↗

bioRxiv2024

The differential virulence of Fusarium oxysporum strains causing corneal infections and plant diseases is associated with accessory chromosome composition

Fusarium oxysporum is a cross-kingdom pathogen. While some strains cause disseminated fusariosis and blinding corneal infections in humans, others are responsible for devastating vascular wilt diseases in plants. To better understand the distinct adaptations of F. oxysporum to animal or plant hosts, we conducted a comparative phenotypic and genetic analysis of two strains: MRL8996 (isolated from a keratitis patient) and Fol4287 (isolated from a wilted tomato [Solanum lycopersicum]). Infection of mouse corneas and tomato plants revealed that, while both strains cause symptoms in both hosts, MRL8996 caused more severe corneal disease in mice, whereas Fol4287 induced more pronounced wilting symptoms in tomato plants. In vitro assays using abiotic stress treatments revealed that the human pathogen MRL8996 was better adapted to elevated temperatures, whereas the plant pathogen Fol4287 was more tolerant to osmotic and cell wall stresses. Both strains displayed broad resistance to antifungal treatment, with MRL8996 exhibiting the paradoxical effect of increased tolerance to higher concentrations of the antifungal caspofungin. We identified a set of accessory chromosomes (ACs) that encode genes with different functions and have distinct transposon profiles between MRL8996 and Fol4287. Interestingly, ACs from both genomes also encode proteins with shared functions, such as chromatin remodeling and post-translational protein modifications. Our phenotypic assays and comparative genomics analyses lay the foundation for future studies correlating genotype with phenotype and for developing targeted antifungals for agricultural and clinical uses. ImportanceFusarium oxysporum is a cross-kingdom fungal pathogen that infects both plants and animals. In addition to causing many devastating wilt diseases, this group of organisms was recently recognized by the World Health Organization as a high-priority threat to human health. Climate change has increased the risk of Fusarium infections, as Fusarium strains are highly adaptable to changing environments. Deciphering fungal adaptation mechanisms is crucial to developing appropriate control strategies. We performed a comparative analysis of Fusarium strains using an animal (mouse) and plant (tomato) host and in vitro conditions that mimic abiotic stress. We also performed comparative genomics analyses to highlight the genetic differences between human and plant pathogens and correlate their phenotypic and genotypic variations. We uncovered important functional hubs shared by plant and human pathogens, such as chromatin modification, transcriptional regulation, and signal transduction, which could be used to identify novel antifungal targets.

microbiology↗

bioRxiv2024

Aspergillus dsRNA virus drives fungal fitness and pathogenicity in the mammalian host

Fungal pathogens pose a significant threat to global health. Aspergillus fumigatus accounts for approximately 65% of all invasive fungal infections in humans, with mortality rates from invasive aspergillosis reaching nearly 50%. Mycoviruses, viruses that infect fungi, can modulate fungal virulence in plant pathogenic fungi, leading to either hypovirulence or hypervirulence. However, their impact on fungal pathogenesis in mammals has remained largely unexplored. Here, utilizing an A. fumigatus strain naturally infected with Aspergillus fumigatus polymycovirus-1M (AfuPmV-1M), we found that the mycovirus confers a significant survival advantage to the fungus under conditions of oxidative stress, heat stress, and within the murine lung. Thus, AfuPmV-1M modulates fungal fitness, resulting in increased virulence and the progression of exacerbated fungal disease. Moreover, antiviral treatment reverses the virus-mediated increase in virulence, representing a promising "antipathogenicity" therapy against virus-bearing pathogenic fungi. Collectively, these findings reveal that mycoviruses act as pivotalbackseat drivers in human fungal diseases, underscoring significant clinical implications and offering promising avenues for novel therapeutic strategies.

microbiology↗

bioRxiv2024

Competitive fungal commensalism mitigates candidiasis pathology

The mycobiota are a critical part of the gut microbiome, but host-fungal interactions and specific functional contributions of commensal fungi to host fitness remain incompletely understood. Here we report the identification of a new fungal commensal, Kazachstania heterogenica var. weizmannii, isolated from murine intestines. K. weizmannii exposure prevented Candida albicans colonization and significantly reduced the commensal C. albicans burden in colonized animals. Following immunosuppression of C. albicans colonized mice, competitive fungal commensalism thereby mitigated fatal candidiasis. Metagenome analysis revealed K. weizmannii presence among human commensals. Our results reveal competitive fungal commensalism within the intestinal microbiota, independent of bacteria and immune responses, that could bear potential therapeutic value for the management of C. albicans-mediated diseases.

immunology↗

bioRxiv2023

Dectin-1/CARD9-induction of the TFEB and TFE3 gene network is dispensable for phagocyte anti-Aspergillus activity in the lung

Myeloid phagocytes of the respiratory immune system, such as neutrophils, monocytes, and alveolar macrophages, are essential for immunity to Aspergillus fumigatus, the most common etiologic agent of mold pneumonia worldwide. Following engulfment of A. fumigatus conidia, fusion of the phagosome with the lysosome, is a critical process for killing conidia. TFEB and TFE3 are transcription factors that regulate lysosomal biogenesis under stress and are activated by inflammatory stimuli in macrophages, but it is unknown whether TFEB and TFE3 contribute to anti-Aspergillus immunity during infection. We found that lung neutrophils express TFEB and TFE3, and their target genes were upregulated during A. fumigatus lung infection. Additionally, A. fumigatus infection induced nuclear accumulation of TFEB and TFE3 in macrophages in a process regulated by Dectin-1 and CARD9 signaling. Genetic deletion of Tfeb and Tfe3 impaired macrophage killing of A. fumigatus conidia. However, in a murine immune competent Aspergillus infection model with genetic deficiency of Tfeb and Tfe3 in hematopoietic cells, we surprisingly found that lung myeloid phagocytes had no defects in conidial phagocytosis or killing. Loss of TFEB and TFE3 did not impact murine survival or clearance of A. fumigatus from the lungs. Our findings indicate that myeloid phagocytes activate TFEB and TFE3 in response to A. fumigatus, and while this pathway promotes macrophage fungicidal activity in vitro, genetic loss can be functionally compensated at the portal of infection in the lung, resulting in no measurable defect in fungal control and host survival.

immunology↗

bioRxiv2023

Maternal exposure to environmental levels of carbamazepine induces mild growth retardation in mouse embryos

As chemical pollution is constantly increasing, the impact on the environment and public health must be investigated. This study focuses on the anticonvulsant drug carbamazepine (CBZ), which is ubiquitously present in the environment. Due to its physicochemical properties and stability during wastewater treatment, CBZ is detected in reclaimed wastewater, surface water and groundwater. In water-scarce regions heavily relying on treated wastewater for crop irrigation, CBZ is detected in arable land, produce and even in humans consuming crops irrigated with recealimed wastewater. Aalthough environmental levels of CBZ are very low, risks associated with unintentional exposure to CBZ are essential to be revealed. In perinatal medicine, CBZ is a teratogen; its prescription to pregnant women increases the risk for fetal malformations. This raises the concern of whether environmental exposure to CBZ may also impact embryogenesis. Studies in zebrafish and chick embryos or in cell culture have indicated negative outcomes upon exposure to low CBZ levels. Yet, these systems do not recapitulate the manner by which human fetuses are exposed to pharmaceuticals via maternal uptake. Here, we employed the mouse model to determine whether maternal exposure to environmental-relevant doses of CBZ will impact embryonic development. No effects on fertility, number of gestation sacs, gross embryonic malformations or fetal survival were detected. Yet, embryos were growth-delayed compared to controls (p=0.0011), as manifested in lower embryonic stage and somite number, earlier morphological features and reduction in mitotically-active cells. This study provides the first evidence for the effect of environmental concentration of CBZ on the developmental kinetics of maternally-exposed mammalian embryos. While the developmental delay was relatively modest, its consistency in high number of biological replicates, together with the known implication of developmental delay on post-natal health, calls for further in-depth risk analyses to reveal the effects of pharmaceuticals released to the environment on public health.

developmental biology↗

bioRxiv2022

Quorum sensing peptidic inhibitor rescue host immune system eradication: a novel QS infectivity mechanism

Subverting the host immune system is a major task for any given pathogen to assure its survival and proliferation. For the opportunistic human pathogen Bacillus cereus (Bc), immune evasion enables the establishment of potent infections. In various species of the Bc group, the pleiotropic regulator PlcR and its cognate cell-cell signaling peptide PapR7 regulates virulence genes expression in response to fluctuations in population density, i.e., a quorum-sensing (QS) system. However, how QS exerts its effects during infections, and whether PlcR confers the immune evading ability remain unclear. Herein, we report how interception of the QS communication in Bc obliterates the ability to control the host immune system. Here we designed a peptide-based QS inhibitor that suppresses PlcR-dependent virulence factor expression and attenuates Bc infectivity in mouse models. We demonstrate that the QS peptidic inhibitor blocks host immune system-mediated eradication by reducing the expression of PlcR-regulated major toxins. Our findings provide the first evidence that Bc infectivity is regulated by QS circuit mediated destruction of the host immunity, thus reveal a new strategy to limit Bc virulence and enhance host defense. This peptidic quorum-quenching agent constitutes readily accessible chemical tool for studying how other pathogen QS systems modulate host immunity and forms a basis for development of anti-infective therapeutics.

microbiology↗